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Yorodumi- EMDB-3108: Structure of the mouse serotonin receptor 5-HT3 in lipid vesicles -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3108 | |||||||||
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Title | Structure of the mouse serotonin receptor 5-HT3 in lipid vesicles | |||||||||
Map data | Reconstruction of the mouse 5-HT3 receptor in lipid vesicles by sub-tomogram averaging. | |||||||||
Sample |
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Function / homology | Function and homology information Neurotransmitter receptors and postsynaptic signal transmission / serotonin-gated monoatomic cation channel activity / serotonin-activated cation-selective channel complex / serotonin receptor signaling pathway / excitatory extracellular ligand-gated monoatomic ion channel activity / serotonin binding / inorganic cation transmembrane transport / cleavage furrow / transmembrane transporter complex / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential ...Neurotransmitter receptors and postsynaptic signal transmission / serotonin-gated monoatomic cation channel activity / serotonin-activated cation-selective channel complex / serotonin receptor signaling pathway / excitatory extracellular ligand-gated monoatomic ion channel activity / serotonin binding / inorganic cation transmembrane transport / cleavage furrow / transmembrane transporter complex / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / presynaptic membrane / postsynaptic membrane / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | subtomogram averaging / cryo EM / negative staining / Resolution: 12.0 Å | |||||||||
Authors | Kudryashev M / Castano-Diez D / Deluz C / Hassaine G / Graf-Meyer A / Vogel H / Stahlberg H | |||||||||
Citation | Journal: Structure / Year: 2016 Title: The Structure of the Mouse Serotonin 5-HT3 Receptor in Lipid Vesicles. Authors: Mikhail Kudryashev / Daniel Castaño-Díez / Cédric Deluz / Gherici Hassaine / Luigino Grasso / Alexandra Graf-Meyer / Horst Vogel / Henning Stahlberg / Abstract: The function of membrane proteins is best understood if their structure in the lipid membrane is known. Here, we determined the structure of the mouse serotonin 5-HT3 receptor inserted in lipid ...The function of membrane proteins is best understood if their structure in the lipid membrane is known. Here, we determined the structure of the mouse serotonin 5-HT3 receptor inserted in lipid bilayers to a resolution of 12 Å without stabilizing antibodies by cryo electron tomography and subtomogram averaging. The reconstruction reveals protein secondary structure elements in the transmembrane region, the extracellular pore, and the transmembrane channel pathway, showing an overall similarity to the available X-ray model of the truncated 5-HT3 receptor determined in the presence of a stabilizing nanobody. Structural analysis of the 5-HT3 receptor embedded in a lipid bilayer allowed the position of the membrane to be determined. Interactions between the densely packed receptors in lipids were visualized, revealing that the interactions were maintained by the short horizontal helices. In combination with methodological improvements, our approach enables the structural analysis of membrane proteins in response to voltage and ligand gating. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3108.map.gz | 7.2 MB | EMDB map data format | |
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Header (meta data) | emd-3108-v30.xml emd-3108.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | EMD-3108.tif | 327.3 KB | ||
Masks | emd_3108_msk_1.map | 8 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3108 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3108 | HTTPS FTP |
-Validation report
Summary document | emd_3108_validation.pdf.gz | 270.5 KB | Display | EMDB validaton report |
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Full document | emd_3108_full_validation.pdf.gz | 269.6 KB | Display | |
Data in XML | emd_3108_validation.xml.gz | 5.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3108 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3108 | HTTPS FTP |
-Related structure data
Similar structure data | |
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EM raw data | EMPIAR-10046 (Title: Cryo electron tomography of mouse 5-HT3 receptors in lipid vesicles Data size: 158.8 Data #1: Tilt series of the 5-HT3 receptors reconstituted to lipid vesicles [class averages]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3108.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the mouse 5-HT3 receptor in lipid vesicles by sub-tomogram averaging. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.67 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Segmentation: mask for the final visualization, contains one pentamer
Annotation | mask for the final visualization, contains one pentamer | ||||||||||||
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File | emd_3108_msk_1.map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Mouse serotonin receptor 5-HT3
Entire | Name: Mouse serotonin receptor 5-HT3 |
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Components |
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-Supramolecule #1000: Mouse serotonin receptor 5-HT3
Supramolecule | Name: Mouse serotonin receptor 5-HT3 / type: sample / ID: 1000 / Oligomeric state: pentamer / Number unique components: 1 |
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Molecular weight | Theoretical: 244 MDa |
-Macromolecule #1: 5-hydroxytryptamine receptor
Macromolecule | Name: 5-hydroxytryptamine receptor / type: protein_or_peptide / ID: 1 / Name.synonym: 5-HT3 / Details: Protein reconstituted into lipid vesicles. / Number of copies: 5 / Oligomeric state: pentamer / Recombinant expression: Yes |
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Source (natural) | Organism: Mus musculus (house mouse) / synonym: Mouse / Location in cell: Plasma membrane |
Molecular weight | Theoretical: 244 MDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: T-REx-293 cells / Recombinant plasmid: pcDNA5/TO |
Sequence | UniProtKB: 5-hydroxytryptamine receptor 3A |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Staining | Type: NEGATIVE / Details: Cryo-preparation |
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Grid | Details: Holey carbon grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 90 K / Instrument: LEICA EM GP / Method: Blot for 2 second before plunding |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Legacy - Astigmatism: corrected at high magnification |
Details | tomograms acquired without the energy filtration |
Date | Dec 1, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 46 / Average electron dose: 41 e/Å2 / Details: 46 tomograms were selected for processing |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | Particles were automatically picked from the surface of the vesicles in CTF-corrected cryo-electron tomograms. After a rough alignment deep classification into 20 classes was performed including 4 neighbouring pentamers in the alignment mask. Finally the central pentamers from each class were cropped, aligned and averaged resulting in a final structure. |
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Final reconstruction | Applied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: OTHER / Software - Name: IMOD, Dynamo / Number subtomograms used: 16000 |
CTF correction | Details: ctfplotter |
Final 3D classification | Number classes: 20 |